15-78541488-C-T

Variant names:

• chr15-78541488-C-T
• rs4243083
• ENST00000559934.5:n.1045C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000559934.5(PSMA4):​n.1045C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000219 in 196,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00027 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000045 (0 hom.)
• Consequence: PSMA4 ENST00000559934.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 10 publications found

Genes affected

PSMA4 (HGNC:9533): (proteasome 20S subunit alpha 4) This gene encodes a core alpha subunit of the 20S proteosome, which is a highly ordered ring-shaped structure composed of four rings of 28 non-identical subunits. Proteasomes cleave peptides in an ATP- and ubiquitin-dependent manner. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559934.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMA4	NM_002789.6	MANE Select	c.-23-417C>T		intron	N/A	NP_002780.1
	PSMA4	NM_001102667.2		c.-23-417C>T		intron	N/A	NP_001096137.1
	PSMA4	NM_001330676.2		c.-23-417C>T		intron	N/A	NP_001317605.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMA4	ENST00000559934.5	TSL:1	n.1045C>T		non_coding_transcript_exon	Exon 1 of 6
	PSMA4	ENST00000044462.12	TSL:1 MANE Select	c.-23-417C>T		intron	N/A	ENSP00000044462.7
	PSMA4	ENST00000413382.6	TSL:1	c.-73-417C>T		intron	N/A	ENSP00000402118.2

Frequencies

GnomAD3 genomes AF: 0.000243 AC: 37 AN: 152022 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000870

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000450 AC: 2 AN: 44410 Hom.: 0 Cov.: 0 AF XY: 0.0000420 AC XY: 1 AN XY: 23804

African (AFR) AF: 0.00325 AC: 1 AN: 308

American (AMR) AF: 0.00 AC: 0 AN: 3004

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 676

East Asian (EAS) AF: 0.00 AC: 0 AN: 614

South Asian (SAS) AF: 0.00 AC: 0 AN: 8108

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2178

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 140

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 27000

Other (OTH) AF: 0.000420 AC: 1 AN: 2382

GnomAD4 genome AF: 0.000269 AC: 41 AN: 152140 Hom.: 0 Cov.: 31 AF XY: 0.000282 AC XY: 21 AN XY: 74382

African (AFR) AF: 0.000963 AC: 40 AN: 41516

American (AMR) AF: 0.0000654 AC: 1 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10576

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67972

Other (OTH) AF: 0.00 AC: 0 AN: 2108

Alfa AF: 0.00 Hom.: 1186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.33
DANN	Benign	0.95
PhyloP100		-1.7
PromoterAI		-0.031	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4243083; hg19: chr15-78833830;